I apologize in advance for this lengthy post:
Have a 2003 1600. Bike settings: Carb - bsr40 / main: dynojet 195 w/needle on 4th from top position / pilot: mikuni 40.
After market K&N air filter and box and cobra drag pipes with baffles installed. Everything else stock.

I have been chasing a carb cough (pop back) since buying the bike. It will only happen from off idle and that's it. I have put in a larger pilot (Mikuni 40), and per skwearpeg's advice moved my needle clip to the 4th position from the top (which really helped). However, I will still get a carb cough to a full blown backfire through the carb (flames and all when air cleaner is removed) when giving it quick throttle inputs from off idle. I originally figured this was because of a lean condition with the fueling but I'm beginning to think otherwise. In an attempt to get this cough to go away I moved the the needle clip all the way to the 6th position to try and eliminate the cough (knowing that it would be too rich) but in doing so noticed no difference than from when the clip was in the 4th position. The needle clip was originally in the 3rd position and when going to the 4th the change in the frequency of the cough was dramatically reduced. Here's what I'm noticing about the bike right now, any input would be appreciated:

-No matter how rich I set the carb settings I will still get the cough/carb backfire (occasionally)
-Going from the 3rd position to 4th position on needle made dramatic improvements but going to 5th and 6th positions would not make any noticeable difference in cough frequency.
-Accelerator pump working as it should
-No vacuum or air leaks that I can detect (sprayed starting fluid with no results)
-New spark plugs and wires
-Removed and cleaned carb and all jets and inspected all parts for proper performance
-Set float level 4mm above mating surface
-Ran heavy concentration of seafoam through a tank of gas
-Bike seems to run good in all other aspects

Could I be experiencing a case of SVS even though this is a 1600 and not a 1700?
-rear cylinder sounds different than the front cylinder when listening to the exhaust
-rear cylinder makes a frequent popping noise that can be felt as VERY high pressure pulses out of the exhaust tip
-front cylinder does not make this distinct popping noise and has a nice even pressure while running
-160 psi compression on rear cylinder / 170 psi compression on front cylinder
-performed the piece of paper at the exhuast tips test with mixed results: The piece of paper would be sucked into the exhaust occasionally on both cyclinders with the rear being worse. The high pressure popping coming from the rear cylinder would be so intense it would actually rip the paper in half and blow it a couple feet away from bike. I don't know why the paper would be sucked in occasionlly on the front cylinder because that one sounds much more even with no popping or abnormal pressure pulses coming from it. I could have been doing something wrong.
-sometimes while riding at slow speeds (but high rpm's) in first and second gear a noticeable change in the amount of engine braking can be felt when letting of the throttle. Sometimes the engine braking will be strong and then other times not nearly as strong and the exhaust note sounds different or fluffy (fluffy is the best adjective I've come across while reading through many of these posts regarding SVS).

Other than this the bike seems to run strong. Even when I'm experiencing the difference in engine braking levels as soon as I get back on the throttle the bike responds well. I haven't experienced any other symptoms that are usually related with SVS such as the bike seeming to run on one cylinder or crappy altogether. Because I've tried making the carb as rich as possible to eliminate the cough (really just to determine that the cough was a fuel related issue and nothing else) with no success I'm beginning to think it might have something to do with the valves. Any input or advice would be greatly appreciated. Thanks.

try increasing the idle rpm. worked for me.....

Like Flashback mentioned, be sure your idle is set around 900rpms. Its what the factory recommends. If you have the idle down to around 650 for the whole potato potato thing, you're not doing your bike any favors. Put the clip back in the fourth groove. Set the PMS about 2 3/8 out, and leave it be. Roadies with the stock CV carb, don't like to be blipped.

The pressure will feel different on each pipe, because one has more of a bend in it, then the other.

I'd check your exhaust gaskets for leaks, and replace them with the yamaha OEM's if need be. Recheck the torque on them a couple of times when the bike is cold, after your first few rides.

Most likely not your valves. Your '03 has the upgraded oil drive gear shaft so not likely lifter droop. A compression check would suffice.

I was not ready to give up just yet and leave well enough alone. So after reading more posts on here I came across one that mentioned an elusive intake manifold leak that was only discovered after spraying the intake with starting fluid from the left side of the bike near the fuel pump. The leak was at the back of the manifold so when spraying from the carb side the leak could not be detected. I realized I had not done this so decided to go out and give it a try. Sure as sh*t I was able to get the bike to start to stumble. Hopefully this is why the bike is coughing/backfiring through the carb when giving quick throttle inputs from off idle. I understand that these bikes don't like being blipped but I've also read plenty of posts on here from people who said they have absolutely zero problems when blipping their throttle with their carbs dialed in.

Now I need to get myself a new manifold. Does Curt still sell his ported manifolds on here? If not, where would be the next best place to purchase one without paying dealership prices?

I'd see if I could apply a thick coat of black silicone gasket sealant to the apparent leak and see how it responds. Perhaps it's just not on as tight as it should be rather than a cracked manifold? May be an easy fix...

I don't think Curt is porting anymore. His health won't let him.